Project Members:
Prof. Dr. Verena Keitel
verena.keitel@med.uni-duesseldorf.de
Universitätsklinikum Düsseldorf
Dr. Maria Reich
maria.reich@uni-duesseldorf.de
Universitätsklinikum Düsseldorf
Prof. Dr. Mathias Heikenwälder
m.heikenwaelder@dkfz-heidelberg.de
DKFZ Heidelberg
QBiC contacts:
Dr. Gisela Gabernet
Bioinformatics project manager
gisela.gabernet@qbic.uni-tuebingen.de
The pathway analysis results are stored under results/pathway_analysis, and explained in this section.
The plot below summarizes the pathways that were found significantly enriched in DE genes for each contrast (padj value < 0.05). Only contrasts for which an enriched pathway was found are shown. Both KEGG pathways and REACTOME (REAC) pathways were considered.
Hover over the dots to reveal the pathway names.
Table summarizing all the enriched pathways. The results can also be inspected on the browser query under this link: https://biit.cs.ut.ee/gplink/l/WvtPn1HzTm. This table can be also found under results/pathway_analysis.
| Contrast | Pathway name | Pathway code | DE genes in pathway (N) | Total genes in pathway (N) | Fraction of DE genes in pathway | Padj value (pathway enrichment) | DE genes names |
|---|---|---|---|---|---|---|---|
| DE_genes_Cholangiocytes_TGR5_vs_MDR2KO | Innate Immune System | REAC:R-MMU-168249 | 11 | 976 | 0.0113 | 0.0441 | Hspa8,Pigr,Dynll1,Actg1,Txnip,Dsp,Ubc,Ahsg,Lcn2,Vtn,Cxcl1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Type I diabetes mellitus | KEGG:04940 | 10 | 62 | 0.161 | 9.9e-11 | H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,Il1b,Cpe,H2-Eb1,H2-Aa,H2-Ab1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Graft-versus-host disease | KEGG:05332 | 9 | 55 | 0.164 | 1.27e-09 | H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,Il1b,H2-Eb1,H2-Aa,H2-Ab1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Antigen processing and presentation | KEGG:04612 | 10 | 81 | 0.123 | 1.6e-09 | H2-D1,H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,H2-Eb1,Cd74,H2-Aa,H2-Ab1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Allograft rejection | KEGG:05330 | 8 | 55 | 0.145 | 4.98e-08 | H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,H2-Eb1,H2-Aa,H2-Ab1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Autoimmune thyroid disease | KEGG:05320 | 8 | 70 | 0.114 | 3.62e-07 | H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,H2-Eb1,H2-Aa,H2-Ab1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Viral myocarditis | KEGG:05416 | 8 | 80 | 0.1 | 1.06e-06 | H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,H2-Eb1,H2-Aa,H2-Ab1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Epstein-Barr virus infection | KEGG:05169 | 11 | 221 | 0.0498 | 2.63e-06 | H2-D1,H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Gadd45b,Jun,H2-Eb1,H2-Aa,H2-Ab1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Phagosome | KEGG:04145 | 10 | 173 | 0.0578 | 2.92e-06 | H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,C3,H2-Eb1,H2-Aa,H2-Ab1,Fcgr2b |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Cell adhesion molecules | KEGG:04514 | 9 | 162 | 0.0556 | 2.13e-05 | H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,Alcam,H2-Eb1,H2-Aa,H2-Ab1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Human T-cell leukemia virus 1 infection | KEGG:05166 | 10 | 236 | 0.0424 | 5.36e-05 | H2-D1,H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Jun,H2-Eb1,H2-Aa,H2-Ab1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Leishmaniasis | KEGG:05140 | 6 | 70 | 0.0857 | 0.000197 | Il1b,C3,Jun,H2-Eb1,H2-Aa,H2-Ab1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Staphylococcus aureus infection | KEGG:05150 | 7 | 116 | 0.0603 | 0.000293 | C1qb,C3,H2-Eb1,C1qa,H2-Aa,H2-Ab1,Fcgr2b |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Herpes simplex virus 1 infection | KEGG:05168 | 12 | 436 | 0.0275 | 0.00035 | H2-D1,H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Il1b,C3,H2-Eb1,Cd74,H2-Aa,H2-Ab1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Coronavirus disease - COVID-19 | KEGG:05171 | 9 | 239 | 0.0377 | 0.000544 | Rpl37a,Rps29,Rps18,Rps2,Il1b,C1qb,C3,Jun,C1qa |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Rheumatoid arthritis | KEGG:05323 | 6 | 84 | 0.0714 | 0.000576 | Il1b,Cxcl2,Jun,H2-Eb1,H2-Aa,H2-Ab1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Inflammatory bowel disease | KEGG:05321 | 5 | 61 | 0.082 | 0.00179 | Il1b,Jun,H2-Eb1,H2-Aa,H2-Ab1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Kaposi sarcoma-associated herpesvirus infection | KEGG:05167 | 8 | 217 | 0.0369 | 0.00217 | H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,Cxcl2,C3,Jun |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Tuberculosis | KEGG:05152 | 7 | 179 | 0.0391 | 0.00495 | Il1b,C3,H2-Eb1,Cd74,H2-Aa,H2-Ab1,Fcgr2b |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Pertussis | KEGG:05133 | 5 | 76 | 0.0658 | 0.0052 | Il1b,C1qb,C3,Jun,C1qa |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Systemic lupus erythematosus | KEGG:05322 | 6 | 141 | 0.0426 | 0.0108 | C1qb,C3,H2-Eb1,C1qa,H2-Aa,H2-Ab1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Viral carcinogenesis | KEGG:05203 | 7 | 216 | 0.0324 | 0.016 | H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,C3,Jun |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Chagas disease | KEGG:05142 | 5 | 102 | 0.049 | 0.021 | Il1b,C1qb,C3,Jun,C1qa |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Th17 cell differentiation | KEGG:04659 | 5 | 103 | 0.0485 | 0.0219 | Il1b,Jun,H2-Eb1,H2-Aa,H2-Ab1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Human immunodeficiency virus 1 infection | KEGG:05170 | 7 | 228 | 0.0307 | 0.0223 | H2-D1,H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Jun |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Asthma | KEGG:05310 | 3 | 25 | 0.12 | 0.0279 | H2-Eb1,H2-Aa,H2-Ab1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Cellular senescence | KEGG:04218 | 6 | 171 | 0.0351 | 0.0308 | H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,Gadd45b |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Human cytomegalovirus infection | KEGG:05163 | 7 | 245 | 0.0286 | 0.0345 | H2-D1,H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Il1b |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Endosomal/Vacuolar pathway | REAC:R-MMU-1236977 | 5 | 29 | 0.172 | 9.43e-05 | H2-K1,B2m,H2-Q6,H2-T23,H2-Q7 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | DAP12 signaling | REAC:R-MMU-2424491 | 6 | 55 | 0.109 | 9.85e-05 | H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Tyrobp |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | DAP12 interactions | REAC:R-MMU-2172127 | 6 | 64 | 0.0938 | 0.000246 | H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Tyrobp |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | ER-Phagosome pathway | REAC:R-MMU-1236974 | 5 | 37 | 0.135 | 0.000335 | H2-K1,B2m,H2-Q6,H2-T23,H2-Q7 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Antigen Presentation: Folding, assembly and peptide loading of class I MHC | REAC:R-MMU-983170 | 5 | 45 | 0.111 | 0.000911 | H2-K1,B2m,H2-Q6,H2-T23,H2-Q7 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Post-translational protein phosphorylation | REAC:R-MMU-8957275 | 6 | 105 | 0.0571 | 0.00448 | Spp1,Prss23,Apoe,C3,Lgals1,Ccn1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) | REAC:R-MMU-381426 | 6 | 111 | 0.0541 | 0.00616 | Spp1,Prss23,Apoe,C3,Lgals1,Ccn1 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | REAC:R-MMU-198933 | 7 | 177 | 0.0395 | 0.0093 | H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Cd300lg,C3 |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Innate Immune System | REAC:R-MMU-168249 | 15 | 976 | 0.0154 | 0.0239 | H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Cd93,Il1b,Clu,Lyz2,C1qb,Cxcl2,C3,Jun,Tyrobp,C1qa |
| DE_genes_Endothelial_TGR5_vs_MDR2KO | Antigen processing-Cross presentation | REAC:R-MMU-1236975 | 5 | 95 | 0.0526 | 0.0355 | H2-K1,B2m,H2-Q6,H2-T23,H2-Q7 |
| DE_genes_Endothelial_vascular_TGR5_vs_MDR2KO | Human T-cell leukemia virus 1 infection | KEGG:05166 | 9 | 236 | 0.0381 | 0.00334 | H2-D1,Fos,H2-K1,Icam1,Jun,H2-Q7,Ccnd2,Egr1,Zfp36 |
| DE_genes_Endothelial_vascular_TGR5_vs_MDR2KO | Fluid shear stress and atherosclerosis | KEGG:05418 | 7 | 141 | 0.0496 | 0.00493 | Gstm1,Fos,Icam1,Jun,Ass1,Dusp1,Klf2 |
| DE_genes_Endothelial_vascular_TGR5_vs_MDR2KO | Kaposi sarcoma-associated herpesvirus infection | KEGG:05167 | 8 | 217 | 0.0369 | 0.0117 | H2-D1,Fos,H2-K1,Icam1,Jun,Lyn,H2-Q7,Zfp36 |
| DE_genes_Endothelial_vascular_TGR5_vs_MDR2KO | Scavenging by Class H Receptors | REAC:R-MMU-3000497 | 2 | 3 | 0.667 | 0.0425 | Sparc,Stab2 |
| DE_genes_Fibroblasts_TGR5_vs_MDR2KO | Antigen processing and presentation | KEGG:04612 | 4 | 81 | 0.0494 | 0.00934 | B2m,H2-D1,H2-K1,Cd74 |
| DE_genes_Hepatocytes_TGR5_vs_MDR2KO | Metabolic pathways | KEGG:01100 | 25 | 1531 | 0.0163 | 0.000128 | Scd1,Aox3,Car3,Elovl3,Glud1,Nnmt,Hsd3b5,Hpd,Uox,Ugp2,Acat1,Got1,Ephx2,Gapdh,Acaa1b,Selenbp2,Me1,Sds,mt-Nd4l,Gstm3,mt-Nd5,Ptgds,Cyp2c29,Cyp2e1,Glul |
| DE_genes_Hepatocytes_TGR5_vs_MDR2KO | Carbon metabolism | KEGG:01200 | 6 | 123 | 0.0488 | 0.0094 | Glud1,Acat1,Got1,Gapdh,Me1,Sds |
| DE_genes_Hepatocytes_TGR5_vs_MDR2KO | Nitrogen metabolism | KEGG:00910 | 3 | 17 | 0.176 | 0.0121 | Car3,Glud1,Glul |
| DE_genes_Hepatocytes_TGR5_vs_MDR2KO | PPAR signaling pathway | KEGG:03320 | 5 | 89 | 0.0562 | 0.0187 | Scd1,Fabp1,Ubc,Acaa1b,Me1 |
| DE_genes_Hepatocytes_TGR5_vs_MDR2KO | Arginine biosynthesis | KEGG:00220 | 3 | 20 | 0.15 | 0.0201 | Glud1,Got1,Glul |
| DE_genes_Hepatocytes_TGR5_vs_MDR2KO | Complement and coagulation cascades | KEGG:04610 | 5 | 91 | 0.0549 | 0.0208 | F12,Serpina1e,Clu,Vtn,C3 |
| DE_genes_Hepatocytes_TGR5_vs_MDR2KO | Fatty acid metabolism | KEGG:01212 | 4 | 62 | 0.0645 | 0.0486 | Scd1,Elovl3,Acat1,Acaa1b |
| DE_genes_Hepatocytes_TGR5_vs_MDR2KO | Platelet degranulation | REAC:R-MMU-114608 | 8 | 110 | 0.0727 | 0.000141 | Rarres2,Ahsg,Cd63,A1bg,Tagln2,Clu,Anxa5,Actg1 |
| DE_genes_Hepatocytes_TGR5_vs_MDR2KO | Response to elevated platelet cytosolic Ca2+ | REAC:R-MMU-76005 | 8 | 115 | 0.0696 | 0.000199 | Rarres2,Ahsg,Cd63,A1bg,Tagln2,Clu,Anxa5,Actg1 |
| DE_genes_Hepatocytes_TGR5_vs_MDR2KO | Metabolism | REAC:R-MMU-1430728 | 26 | 1678 | 0.0155 | 0.00152 | Scd1,Fabp1,Car3,Elovl3,Glud1,Akr1c19,Nnmt,Hsd3b5,Hpd,Ugp2,Rbp4,Acat1,Got1,Ephx2,Gapdh,Thrsp,Me1,Bsg,Fitm1,Sds,Apom,mt-Nd5,Serpina6,Ptgds,Cyp2e1,Glul |
| DE_genes_Hepatocytes_TGR5_vs_MDR2KO | Post-translational protein phosphorylation | REAC:R-MMU-8957275 | 6 | 105 | 0.0571 | 0.0166 | Ahsg,Spp1,Ccn1,Mfge8,Cp,C3 |
| DE_genes_Hepatocytes_TGR5_vs_MDR2KO | Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) | REAC:R-MMU-381426 | 6 | 111 | 0.0541 | 0.0227 | Ahsg,Spp1,Ccn1,Mfge8,Cp,C3 |
| DE_genes_Hepatocytes_TGR5_vs_MDR2KO | Platelet activation, signaling and aggregation | REAC:R-MMU-76002 | 8 | 239 | 0.0335 | 0.0421 | Rarres2,Ahsg,Cd63,A1bg,Tagln2,Clu,Anxa5,Actg1 |
| DE_genes_HSC_TGR5_vs_MDR2KO | Antigen processing and presentation | KEGG:04612 | 8 | 81 | 0.0988 | 7.15e-07 | B2m,H2-D1,H2-K1,Hspa1a,Cd74,H2-Aa,H2-Eb1,H2-Ab1 |
| DE_genes_HSC_TGR5_vs_MDR2KO | Staphylococcus aureus infection | KEGG:05150 | 7 | 116 | 0.0603 | 0.000194 | Krt18,H2-Aa,H2-Eb1,H2-Ab1,C1qb,C1qa,C1qc |
| DE_genes_HSC_TGR5_vs_MDR2KO | Complement and coagulation cascades | KEGG:04610 | 6 | 91 | 0.0659 | 0.000646 | Clu,F3,C7,C1qb,C1qa,C1qc |
| DE_genes_HSC_TGR5_vs_MDR2KO | Systemic lupus erythematosus | KEGG:05322 | 7 | 141 | 0.0496 | 0.00071 | C7,H2-Aa,H2-Eb1,H2-Ab1,C1qb,C1qa,C1qc |
| DE_genes_HSC_TGR5_vs_MDR2KO | Graft-versus-host disease | KEGG:05332 | 5 | 55 | 0.0909 | 0.000804 | H2-D1,H2-K1,H2-Aa,H2-Eb1,H2-Ab1 |
| DE_genes_HSC_TGR5_vs_MDR2KO | Allograft rejection | KEGG:05330 | 5 | 55 | 0.0909 | 0.000804 | H2-D1,H2-K1,H2-Aa,H2-Eb1,H2-Ab1 |
| DE_genes_HSC_TGR5_vs_MDR2KO | Type I diabetes mellitus | KEGG:04940 | 5 | 62 | 0.0806 | 0.00145 | H2-D1,H2-K1,H2-Aa,H2-Eb1,H2-Ab1 |
| DE_genes_HSC_TGR5_vs_MDR2KO | Autoimmune thyroid disease | KEGG:05320 | 5 | 70 | 0.0714 | 0.00263 | H2-D1,H2-K1,H2-Aa,H2-Eb1,H2-Ab1 |
| DE_genes_HSC_TGR5_vs_MDR2KO | Viral myocarditis | KEGG:05416 | 5 | 80 | 0.0625 | 0.00502 | H2-D1,H2-K1,H2-Aa,H2-Eb1,H2-Ab1 |
| DE_genes_HSC_TGR5_vs_MDR2KO | Prion disease | KEGG:05020 | 8 | 261 | 0.0307 | 0.00516 | mt-Nd4l,mt-Nd5,mt-Nd3,C7,Hspa1a,C1qb,C1qa,C1qc |
| DE_genes_HSC_TGR5_vs_MDR2KO | Rheumatoid arthritis | KEGG:05323 | 5 | 84 | 0.0595 | 0.00635 | Jun,Mmp3,H2-Aa,H2-Eb1,H2-Ab1 |
| DE_genes_HSC_TGR5_vs_MDR2KO | Epstein-Barr virus infection | KEGG:05169 | 7 | 221 | 0.0317 | 0.0126 | B2m,H2-D1,H2-K1,Jun,H2-Aa,H2-Eb1,H2-Ab1 |
| DE_genes_HSC_TGR5_vs_MDR2KO | Human T-cell leukemia virus 1 infection | KEGG:05166 | 7 | 236 | 0.0297 | 0.0189 | B2m,H2-D1,H2-K1,Jun,H2-Aa,H2-Eb1,H2-Ab1 |
| DE_genes_HSC_TGR5_vs_MDR2KO | Coronavirus disease - COVID-19 | KEGG:05171 | 7 | 239 | 0.0293 | 0.0204 | Rps2,Jun,C7,Mmp3,C1qb,C1qa,C1qc |
| DE_genes_HSC_TGR5_vs_MDR2KO | Inflammatory bowel disease | KEGG:05321 | 4 | 61 | 0.0656 | 0.0238 | Jun,H2-Aa,H2-Eb1,H2-Ab1 |
| DE_genes_HSC_TGR5_vs_MDR2KO | Asthma | KEGG:05310 | 3 | 25 | 0.12 | 0.0238 | H2-Aa,H2-Eb1,H2-Ab1 |
| DE_genes_HSC_TGR5_vs_MDR2KO | Leishmaniasis | KEGG:05140 | 4 | 70 | 0.0571 | 0.0403 | Jun,H2-Aa,H2-Eb1,H2-Ab1 |
| DE_genes_HSC_TGR5_vs_MDR2KO | Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) | REAC:R-MMU-381426 | 7 | 111 | 0.0631 | 0.00027 | Spp1,Penk,Igfbp6,Gpc3,Ahsg,Ccn1,Igfbp3 |
| DE_genes_HSC_TGR5_vs_MDR2KO | Post-translational protein phosphorylation | REAC:R-MMU-8957275 | 6 | 105 | 0.0571 | 0.00305 | Spp1,Penk,Gpc3,Ahsg,Ccn1,Igfbp3 |
| DE_genes_HSC_TGR5_vs_MDR2KO | Innate Immune System | REAC:R-MMU-168249 | 15 | 976 | 0.0154 | 0.00995 | B2m,Ubc,H2-K1,Gsn,Clu,Jun,Ahsg,C7,Ttr,Hspa1a,Tyrobp,Lyz2,C1qb,C1qa,C1qc |
| DE_genes_HSC_TGR5_vs_MDR2KO | Regulation of Complement cascade | REAC:R-MMU-977606 | 5 | 99 | 0.0505 | 0.0316 | Clu,C7,C1qb,C1qa,C1qc |
| DE_genes_HSC_TGR5_vs_MDR2KO | Complement cascade | REAC:R-MMU-166658 | 5 | 109 | 0.0459 | 0.0498 | Clu,C7,C1qb,C1qa,C1qc |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Coronavirus disease - COVID-19 | KEGG:05171 | 23 | 239 | 0.0962 | 6.04e-13 | Fau,Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rps5,Rpl6,Rpl28,Rpl36,Rplp0,Nfkbia,Tnf,Il1b,Rps18,C8g,Fgb,C6,Cxcl10,Fgg |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Ribosome | KEGG:03010 | 15 | 137 | 0.109 | 7.33e-09 | Fau,Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rps5,Rpl6,Rpl28,Rpl36,Rplp0,Rps18 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | NF-kappa B signaling pathway | KEGG:04064 | 10 | 104 | 0.0962 | 4.22e-05 | Gadd45b,Bcl2a1b,Cd14,Ccl4,Cxcl2,Nfkbia,Tnf,Il1b,Cxcl1,Icam1 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | PPAR signaling pathway | KEGG:03320 | 9 | 89 | 0.101 | 0.000106 | Fabp1,Apoa2,Apoc3,Scp2,Scd1,Hmgcs2,Apoa1,Lpl,Dbi |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Complement and coagulation cascades | KEGG:04610 | 9 | 91 | 0.0989 | 0.000128 | Serpina1d,Serpina1c,Serpina1e,C8g,Serpina1a,Serpina1b,Fgb,C6,Fgg |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Viral protein interaction with cytokine and cytokine receptor | KEGG:04061 | 9 | 92 | 0.0978 | 0.00014 | Cx3cr1,Ccl4,Cxcl2,Tnf,Ccl3,Cxcl13,Cxcl1,Ccr2,Cxcl10 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Cholesterol metabolism | KEGG:04979 | 7 | 49 | 0.143 | 0.000162 | Apoa2,Apoe,Apoc3,Angptl3,Apoh,Apoa1,Lpl |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Rheumatoid arthritis | KEGG:05323 | 8 | 84 | 0.0952 | 0.000667 | Il1a,Cxcl2,Tnf,Acp5,Ccl3,Il1b,Cxcl1,Icam1 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Fluid shear stress and atherosclerosis | KEGG:05418 | 9 | 141 | 0.0638 | 0.00459 | Il1a,Tnf,Il1b,Mgst1,Ass1,Icam1,Gsta3,Cdh5,Gstm1 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Legionellosis | KEGG:05134 | 6 | 60 | 0.1 | 0.00729 | Cd14,Cxcl2,Nfkbia,Tnf,Il1b,Cxcl1 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | IL-17 signaling pathway | KEGG:04657 | 7 | 88 | 0.0795 | 0.00811 | Cxcl2,Nfkbia,Tnf,Il1b,Cxcl1,Fosb,Cxcl10 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Toll-like receptor signaling pathway | KEGG:04620 | 7 | 98 | 0.0714 | 0.016 | Cd14,Ccl4,Nfkbia,Tnf,Ccl3,Il1b,Cxcl10 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Cytokine-cytokine receptor interaction | KEGG:04060 | 12 | 287 | 0.0418 | 0.0163 | Cx3cr1,Ccl4,Il1a,Cxcl2,Tnf,Ccl3,Cxcl13,Il1b,Cxcl1,Gdf15,Ccr2,Cxcl10 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Amoebiasis | KEGG:05146 | 7 | 103 | 0.068 | 0.0218 | Cd14,Cxcl2,Tnf,Il1b,Cxcl1,C8g,Arg1 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | TNF signaling pathway | KEGG:04668 | 7 | 109 | 0.0642 | 0.0309 | Cxcl2,Nfkbia,Tnf,Il1b,Cxcl1,Icam1,Cxcl10 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Chemokine signaling pathway | KEGG:04062 | 9 | 187 | 0.0481 | 0.039 | Cx3cr1,Ccl4,Cxcl2,Nfkbia,Ccl3,Cxcl13,Cxcl1,Ccr2,Cxcl10 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Graft-versus-host disease | KEGG:05332 | 5 | 55 | 0.0909 | 0.0456 | Il1a,H2-T23,Tnf,Il1b,H2-Q10 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | SRP-dependent cotranslational protein targeting to membrane | REAC:R-MMU-1799339 | 12 | 89 | 0.135 | 8.62e-08 | Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | REAC:R-MMU-975956 | 12 | 91 | 0.132 | 1.12e-07 | Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Formation of a pool of free 40S subunits | REAC:R-MMU-72689 | 12 | 98 | 0.122 | 2.71e-07 | Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | L13a-mediated translational silencing of Ceruloplasmin expression | REAC:R-MMU-156827 | 12 | 108 | 0.111 | 8.48e-07 | Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | GTP hydrolysis and joining of the 60S ribosomal subunit | REAC:R-MMU-72706 | 12 | 109 | 0.11 | 9.44e-07 | Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) | REAC:R-MMU-975957 | 12 | 112 | 0.107 | 1.29e-06 | Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Nonsense-Mediated Decay (NMD) | REAC:R-MMU-927802 | 12 | 112 | 0.107 | 1.29e-06 | Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Eukaryotic Translation Initiation | REAC:R-MMU-72613 | 12 | 116 | 0.103 | 1.94e-06 | Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Cap-dependent Translation Initiation | REAC:R-MMU-72737 | 12 | 116 | 0.103 | 1.94e-06 | Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Retinoid metabolism and transport | REAC:R-MMU-975634 | 8 | 44 | 0.182 | 8.31e-06 | Apoa2,Apoe,Sdc3,Akr1c6,Ttr,Apoa1,Rbp4,Lpl |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Metabolism of fat-soluble vitamins | REAC:R-MMU-6806667 | 8 | 49 | 0.163 | 2.02e-05 | Apoa2,Apoe,Sdc3,Akr1c6,Ttr,Apoa1,Rbp4,Lpl |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Metabolism | REAC:R-MMU-1430728 | 42 | 1678 | 0.025 | 3.02e-05 | Fabp1,Apoa2,Gnmt,Alb,Apoe,Car3,Acp5,Gchfr,Sdc3,Akr1c6,Fbp1,Adh1,Hpd,Scp2,Otc,Arg1,Aldob,Cyp3a11,Cdo1,Tdo2,Pcbd1,Mgst1,Stard10,Ttr,Ass1,Tst,Gc,Rida,Scd1,Gsta3,Hmgcs2,Aldh1a1,Apoa1,Rbp4,Phyh,Gamt,Lpl,Hilpda,Etfb,Acaa2,Dbi,Cyb5a |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Chemokine receptors bind chemokines | REAC:R-MMU-380108 | 8 | 58 | 0.138 | 7.88e-05 | Cx3cr1,Ccrl2,Ccl4,Cxcl2,Ccl3,Cxcl13,Cxcl1,Cxcl10 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Plasma lipoprotein remodeling | REAC:R-MMU-8963899 | 6 | 25 | 0.24 | 8.59e-05 | Apoa2,Alb,Apoe,Angptl3,Apoa1,Lpl |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | rRNA processing | REAC:R-MMU-72312 | 12 | 168 | 0.0714 | 0.000122 | Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Major pathway of rRNA processing in the nucleolus and cytosol | REAC:R-MMU-6791226 | 12 | 168 | 0.0714 | 0.000122 | Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | rRNA processing in the nucleus and cytosol | REAC:R-MMU-8868773 | 12 | 168 | 0.0714 | 0.000122 | Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Translation | REAC:R-MMU-72766 | 13 | 218 | 0.0596 | 0.00031 | Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Eef2,Rplp0,Rps18 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Chylomicron remodeling | REAC:R-MMU-8963901 | 4 | 10 | 0.4 | 0.000971 | Apoa2,Apoe,Apoa1,Lpl |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Plasma lipoprotein assembly, remodeling, and clearance | REAC:R-MMU-174824 | 7 | 58 | 0.121 | 0.00116 | Apoa2,Alb,Apoe,Angptl3,Apoc4,Apoa1,Lpl |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Metabolism of vitamins and cofactors | REAC:R-MMU-196854 | 11 | 173 | 0.0636 | 0.00121 | Apoa2,Apoe,Acp5,Gchfr,Sdc3,Akr1c6,Ttr,Apoa1,Rbp4,Lpl,Cyb5a |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Binding and Uptake of Ligands by Scavenger Receptors | REAC:R-MMU-2173782 | 8 | 86 | 0.093 | 0.00168 | Alb,Apoe,Marco,Cd163,Apoa1,Hp,Hpx,Ambp |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | G alpha (i) signalling events | REAC:R-MMU-418594 | 15 | 347 | 0.0432 | 0.00243 | Apoa2,Cx3cr1,Rgs10,Apoe,Ccl4,Cxcl2,Sdc3,Akr1c6,Cxcl13,Cxcl1,Ttr,Cxcl10,Apoa1,Rbp4,Lpl |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Visual phototransduction | REAC:R-MMU-2187338 | 8 | 91 | 0.0879 | 0.00257 | Apoa2,Apoe,Sdc3,Akr1c6,Ttr,Apoa1,Rbp4,Lpl |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Platelet degranulation | REAC:R-MMU-114608 | 8 | 110 | 0.0727 | 0.0104 | Alb,Orm1,Cd63,Fgb,Apoh,Apoa1,Fgg,Ahsg |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Plasma lipoprotein assembly | REAC:R-MMU-8963898 | 4 | 18 | 0.222 | 0.0132 | Apoa2,Apoe,Apoc4,Apoa1 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Response to elevated platelet cytosolic Ca2+ | REAC:R-MMU-76005 | 8 | 115 | 0.0696 | 0.0143 | Alb,Orm1,Cd63,Fgb,Apoh,Apoa1,Fgg,Ahsg |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Metabolism of amino acids and derivatives | REAC:R-MMU-71291 | 11 | 240 | 0.0458 | 0.0259 | Gnmt,Hpd,Otc,Arg1,Cdo1,Tdo2,Pcbd1,Ass1,Tst,Rida,Gamt |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | HDL remodeling | REAC:R-MMU-8964058 | 3 | 9 | 0.333 | 0.0352 | Alb,Apoe,Apoa1 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Scavenging by Class A Receptors | REAC:R-MMU-3000480 | 3 | 9 | 0.333 | 0.0352 | Apoe,Marco,Apoa1 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Urea cycle | REAC:R-MMU-70635 | 3 | 10 | 0.3 | 0.0499 | Otc,Arg1,Ass1 |
| DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO | Chylomicron assembly | REAC:R-MMU-8963888 | 3 | 10 | 0.3 | 0.0499 | Apoa2,Apoe,Apoa1 |
For pathway analysis, the R package gprofiler2 v0.2.0 was employed. Graphs were produced in RStudio with R version 4.0.3 (2020-10-10) mainly using the R package ggplot2 v3.3.2. Final reports were produced using the R package rmarkdown v2.6, with knitr v1.30.